Molly's Secret
by Who-Is-Locked-In-The-Blue-Box
Summary: Molly is pregnant, but who's the father?
1. Chapter 1

"Hello Sherlock." he didn't look up from his microscope. "Hello Molly." John said, smiling. Sherlock momentarily glanced at Molly and then turned his head to John. "It was the builder. Nobody noticed the daughter's hair dye."

Sherlock jumped off of his stool and walked out the door in a hurry. John was left there, mouth open looking through the microscope. "Come on John." John followed after him like a lap dog. Molly too was just left standing there. She began to clean up after Sherlock. Just like she always did.

John and Sherlock walked out of St .Bart's and hailed a cab. "Sherlock, that was ...amazing." Sherlock didn't even agree with him. John was worried, even in his worst mood, Sherlock never missed a chance to gloat.

"What's wrong?" Sherlock looked at John. "I was just thinking." John did some deducting of his own "Sherlock, that's not your thinking face. What's wrong?" Sherlock sighed "Molly's pregnant."


	2. Chapter 2

Both men walked into Baker's Street. John put the kettle on and threw teabags into the two cups.

"Sherlock, I need to tell you something." Sherlock placed his fingers on the strings of his violin. He began playing a slow, sad song. "I need to tell you something too John, but first, the kettle has boiled."

John was surprised. Sherlock never told him anything. John made the tea while Sherlock played his violin. John wondered what he was thinking about, they had no cases on at the moment.

Placing the tea on to the coffee table, John invited Sherlock to sit in the arm chair across from his. "I know you're going to be surprised by this..." John drank his tea absentmindedly. "Little you do surprises me anymore." Sherlock interrupted. John put his cup down on the coffee table, a little too harshly. "Could you just listen for one second, this is important." Sherlock doubted that it was important, but ushered him to continue with a nod of his head.

"I think..." John tried to find the right words to say it. "Sherlock, I think that Molly's baby could be mine." Sherlock looked up from his cup of tea, watching John's face to see if he was telling the truth. He was.

"Now that was a surprise." Sherlock eventually said after contemplating what an appropriate response to the situation would be. John lifted his teacup in shaky hands. He didn't know why he was so uneasy. Even at war he wasn't this easily shaken. John thought about having children quite a lot, but he always planned on being married first. Or at least being in a long term relationship.

John was going to do the noble thing. He was going to support the baby, presuming it was of course his. Molly hardly had a reputation for sleeping around.

Sherlock snapped John out of his train of thought. "John?" Sherlock waved his hand infront of John's face. "What? Yes, sorry." "I have something to tell you too." John looked at him curiously. This better not be something stupid like, he found a new type of tobacco ash, John thought to himself, before he eventually said "go on."

Sherlock took in a deep breath. "The baby might be mine."


	3. Chapter 3

"Wait, wait. Are you telling me, that Sherlock... He , ehm... I didn't think that it was possible!"

"It was a surprise for me too." John had phoned L'estrade the next morning.

"And then you...and Molly?!"

John was expecting L'estrade to be surprised. Greg couldn't seem to control his shock. John wasn't sure if he was shocked as in you both slept with Molly! Or shock as in, Sherlock slept with, well anyone!

John continued to explain to L'estrade everything that he knew about the situation. John had slept with Molly after Sherlock drove away yet another of his girlfriends. Molly at the time had just been to her best friend's wedding and was feeling extremely sorry for herself. They both got drunk together and one thing led to another... The morning after, they had both agreed that it would be better if they stayed friends.

Molly's second encounter also involved alcohol, but not on her behalf. It was just after Irene Adler left. Something she said had stuck with Sherlock. He had never "had anyone" as she phrased it. Sherlock got drunk one night and stumbled into St .Bart's. He proposed to Molly that they do a science experiment. Molly of course jumped at the chance(excuse the pun!). Afterwards Sherlock went back to being his usual self towards Molly and she ultimately excepted that that would never change.

"What did she say when she told you?" Greg sounded like a giddy five year old.

"That's the thing. She didn't . Sherlock deduced it. Somehow..."

Greg laughed through the phone.

"L'estrade." Greg still laughed. "L'estrade!"

"Sorry John, it's just.. Nothing is ever simple when it comes to you two."

"You got that right!"

"So how are you going to break it to her? It's not everyday the suspected father has to tell the girl that she's pregnant. Although, you are a doctor."

John managed an obviously fake laugh.

"All my years of medical training. All my years in the army. None of them prepared me for this."

He tried to make it sound light hearted, but John really didn't know what to do.

"Listen Greg, I better go. I need to discuss with Sherlock what our next move will be."

"Okay John. Good luck." L'estrade laughed one more time before he hung up. John whispered to himself "I'm going to need it." Now to talk to Sherlock, he thought. Which is extremely difficult because ever since last night, he had been shutting him out and playing his violin until all hours "thinking".


	4. Chapter 4

John stood outside of Sherlocks bedroom door, which had been firmly shut in his face.

"You can't just ignore this Sherlock, we need to talk to Molly."

No answer.

John pounded his fist against the door.

"Sherlock!"

John shouted above the sound of Sherlocks violin. John knew that he could hear him.

"You're acting like a child!"

John threw his hands up in defeat.

cautiously peeked in the door to see John sitting on the couch massaging his temples.

"Im not interrupting am I?"

John walked over to the old women and enveloped her in a hug, like a child returning home to his mother would.

"You're just the person we need ."


	5. Chapter 5

"Well this is...unexpected."

Mrs. Hudson gently placed her cup of tea onto its saucer.

"It'll be okay dear, we'll talk to Molly."

"But Sherlock won't even talk about it, he has been in his room all day. And I wouldn't know what to say, I mean...What do I say?"

"John, it'll all work out in the end. What's the worst that can happen? Molly's a lovely girl."

John looked at Mrs. Hudson, his eyes looked heavy with sincerity.

"I don't think I'm ready to be a father."

Mrs. Hudson reassuringly put her hand on Johns arm.

"I couldn't imagine a better father for anyone."


	6. Chapter 6

"John, I know what we can do."

John woke up to see a tall man standing over him. If he wasn't already used to Sherlock waking him in the middle of the night, then John would've been frightened by the figure.

Looking at his watch, John turned onto his left side.

"Its four in the morning Sherlock."

Sherlock shook him again so that he couldn't fall back asleep.

"I know what we can do about the Molly... situation."

John turned back onto his right side.

"I'm listening."

Sherlock lent beside Johns bed.

"Okay, here's my plan. We leave. Get out of London and hide somewhere."

Sherlock waited for John to answer. He didn't.

"Then, by the time Molly figures it out, we'll be gone and everything will be fine."

There was a short pause.

"Sherlock, that's ridiculous. We can't do that, we have to take responsibility for our actions."

Sherlock thought for a moment.

"John, look at me. Do you honestly think that I would be a good father? My eating habits are hardly a good example, I play the violin at strange hours of the morning, I smoke. I can hardly take care of myself, nevermind anybody else."

John looked at Sherlock. He seemed sad. Maybe this whole baby thing had really shaken him. Brought him down to reality.

"We have to just take this one step at a time. Molly mightn't even want to keep it. Or maybe she won't want you to be part of its life. Or if she does, then you can learn how to be a good father. We should talk to Molly and see what she thinks, after all, she is the one giving birth."

Sherlock nodded and then walked back to his own room, ready to get some much needed sleep now that John had set his mind at ease.


	7. Chapter 7

"Good morning Sherlock."

Sherlock sat on the couch while John tiredly walked in.

"Hello John."

"So what time do you want to go to at?"

John, who was still in his pyjamas, tried to make the situation sound as lighthearted as possible.

"We have no cases on. Why would we need to go there?"

Frustrated, John flicked on the kettle with enough force to almost snap the button off.

"We need to talk to Molly Sherlock."

Sherlock closed his eyes slowly and let his head lean against the wall gently.

"I know that John."

"Then don't you want to do this sooner rather than later?"

"Later's good."

"Mrs. Hudson is coming with us, I'm going to get dressed, when I come back, we're going."

Sherlock sat up to try and protest, but when he opened his eyes, John was gone.

This was really happening.


	8. Chapter 8

"You hail a cab Sherlock."

"We could always walk. He said, while reluctantly closing the buttons of his jacket.

"With my hip?" tried to lighten the mood. Both men were wound up so tight that they could snap at any moment.

John hailed a cab and let get into the front.

"Can we go to the shop first?"

"Sherlock, you never go to the shop."

"We need milk."

"You never buy milk. Stop wasting time, we're going to tell Molly that she's pregnant and that's the end of it!"

The cab driver uncomfortably cleared his throat.

"Don't worry. He's a doctor." gave them a stern look and told the cabbie where to park outside of .

Taking a deep breath, they stepped out of the cab and walked through the door. They had never seemed so daunting before.


	9. Chapter 9

"Can I have a cigarette first?" John had to drag Sherlock into the morgue, kicking and screaming, before he eventually accepted the inevitable.

John walked into Molly's lab, shortly followed by , who was tightly linking arms with Sherlock.

"Hello Molly." John said, trying to sound as calm as possible. Molly looked up from her microscope and smiled. She hadn't heard them walk in, and it was a happy surprise, as she knew that Sherlock had no cases on and therefor, she doubted anyone would visit her.

"Hello John. Sherlock. And , what're you all doing here?"

answered, noticing that the boys had got a little tongue tied. "We need to talk to you dear. Maybe you should sit down."

Molly pulled up a stool and sat down. "What's this about? It must be important for them to drag you all the way from Baker's Street ."

sighed. "It is important. But I'll let the boys explain."

Sherlock stood beside John. He whispered in John's ear "John, she knows." John waved his hand as if swatting away a fly. "But John. She knows!"

John took a step forward, realizing that Sherlock would be useless in this type of situation.

"Molly, we have to tell you something."

"Okay." She said, nervously pulling at her sleeves.

"We know...Well Sherlock said that... You're pregnant."


	10. Chapter 10

"I told you she knew." Sherlock said, while pacing around the lab.

"Yes thank you Sherlock...Now Molly, I want you to know that whatever happens, we'll support you through the whole thing."

Molly was staring at the floor, and she was wearing a hole in her sleeves, with the amount of tugging that she was doing on them.

"How did you...I didn't..."

"It is fairly easy to deduce pregnancy. Your period is 8 days late, you're bloated and you're for lack of a better term 'moody'. All that mixed with the fact that we...well ye'know...in the last month."

"Right, at always." Molly said, with a hint of venom.

"We wanted you to know that you're not alone dear. What ever you decide to do. We'll stand by you. I couldn't think of better people to look after a child."

Molly looked up for the first time since they had told her the news. She seemed more angry now, than anything else.

"Thanks for the vote of confidence."

Sherlock was right. Moody...

"But it's not Sherlock's...And it's not John's."


	11. Chapter 11

"You could seem less happy Sherlock."

"But John, it's not mine!"

"Aren't you a bit concerned that she won't tell us whos it is?"

Sherlock, took a break from his pacing and looked at John.

"You're dissapointed."

John sat down on his armchair.

"Well, yeah."

John ran his hand through his hair.

"This whole thing, made me think about kids."

"And what was your conclusion?"

"That I want some of my own."

Sherlock nervously sat on the sofa.

"John, I'm really not good at this kind of thing."

"Have you ever thought about having children?"

"John, I really don't..."

"But have you though?"

"No."

"Well, would you ever consider it?"

"I don't think that me and children would work very well together."

"You never know. They say that people change after they have kids."

"John, I really don't..."

"You have to think about these things Sherlock. Because time is passing and you know we're getting old. It won't be too long before it's too late. And then you'll regret it for the rest of your life."

John was talking so fast, that he actually had to catch his breath.

"Are you quite done?"

John realized who he had just almost had a break down infront of. Hardly the best person to talk to about anything personal.

"Sorry."

"John, I think you need to talk to someone about this. But I dont think that I'm the person for the job."

"Right, yes. Sorry."

Everything suddenly went quiet and the only thing John said for that rest of the night was that he was going to bed and that he'd appreciate it if Sherlock didn't play his violin all night.

_**Thank you, everyone, for your continued support. You're the reason that I am continuing this story. Usually I give up half way, but I have a good feeling about this one. Review, please. They make it worth while. And tell me your ideas, I always like to hear them :)**_


	12. Chapter 12

"Molly, this is Mary."

Molly smilled and waddled over to John, who was standing beside his new girl friend.

"Molly Hooper. It's so nice to meet you at last. John has told me so much about you."

Mary politely shook Molly's hand.

"It's nice to meet you too Molly. How far along are you?"

Molly looked down at her bump and smiled.

"I'm due any day now."

"And you're still working? Shouldn't you be on maternity leave?"

Mary looked wide eyed at the short and very heavily pregnant woman. Molly waddled back over to her stool and sat in front of her microscope.

It was so hard for Molly to stand up for long periods of time because her feet had swollen to the size of two watermelons and she was also experiencing back looked worryingly at her.

"Well I work in a hospital, so I suppose, there isn't really a better place to be."

John decided to cut the small talk short.

"I brought Mary here today, because she wanted to meet you."

Mary smiled sweetly. "We could maybe go for lunch or something, if you wanted."

Molly, looked up from her microscope, she didn't seem very impressed. She 'smiled' back at Mary. "Thanks for the offer, but I'm really busy at the moment. I have to finish this before tomorrow. So actually, if you wouldn't mind going, that would be great."

Molly looked back down at her microscope. Mary looked at John, who was just as confused as she was. Molly was always so nice. John wanted to know what was wrong, but from Molly's icy reception, he thought that maybe it would be better just to leave her alone.

"Maybe some other time then." Mary said politely, before her and John left the lab hand-in-hand.


	13. Chapter 13

"I'm sorry about that. Molly's not normally so...Cold."

"It's okay. It's probably just her hormones. Has she still not told you who the father is?"

"No. We don't even know if she's keeping it or not. She wont tell us anything."

"Maybe you should get her some professional advice."

"We've tried that. She wasn't having any of it. She insists nothing is wrong."

Mary sipped on her tea, while holding Johns hand with the other. They were in the cafe of 's, waiting for Sherlock to finish an experiment upstairs.

"Maybe you should get someone who understands to talk to her."

" has tried. I mean she's a woman, we thought maybe that would help, but Molly refused to talk about it."

"But was never pregnant, so Molly probably thinks that she wont understand."

John ran his hand through his hair and then lifted his tea in his free hand.

"I don't know anyone who has been pregnant. Except my mom, but that doesn't help much..."

Mary sighed. "I've been pregnant."

John, looked at Mary, who had suddenly become very self conscious.

"You're only telling me that you have kids now? We've been together for two months. It's kinda something that people usually mention."

Mary looked down at her feet.

"John-"

"Not that I mind. I just would've liked to have known."

"John-"

"I'd like to meet them, if that's okay with you...I mean, if it's too soon that's fine. Or if you don't want me to, then that's cool too."

"John, I don't have kids!" Mary said, with a little more aggression than she probably should've.

"Sorry."

"But you've been pregnant?"

"It was...They...It was a still birth." Mary looked into John's eyes and he could see the hurt that she was feeling. John wrapped his arm around Mary and let her lay her head on his shoulder.

"I'm sorry." He said, gently stroking her arm.

"It's okay. You couldn't have known." Mary was staring into space, not really listening to anything that John was saying when he was trying to incessantly apologize for his insensitivity.

When John dropped Mary home on his way back to Baker Street, he apologized again, before kissing her good night and returning to the taxi.

Mary walked into her one bedroom flat and threw her keys into the bowl beside the door. Lying on her couch, she stared at the ceiling and thought of Josh. Her amazing little boy, who met his end, before he began.


End file.
